------------------------------------------------------------------------------------------------------------------------- Will print the top 5 alignments (based on backbone shifts) for each pairing of chains, as measured by a combination of score and contiguity. Some relevant parameters: HELIX min length: 5 STRAND min length: 3 shift-tolerance = -10 permissible-violations = 4 max-breaks = NIL retain-m = 100 best-n = 100 anglethresh = 0.5 septhresh = 5 min_length = 4 rmsd-tol = 9.9999999999999E12 Legend: score1 [score2] pairings L2ERR {Xbad/Xsig:Xtot} Breaks (score2 is the score from protein2's perspective, not the minimum of the two perspectives as in some earlier printouts.) Recall that "SIMILARITY" refers to similarities over all alignments not just the top ones. ------------------------------------------------------------------------------------------------------------------------- [6198, 382]: Comparing 1v8p_A and 1bgx_T, based on their crossing files. There are 12 (8 H + 4 S) secondary structure elements in 1v8p_A, of which 11 satisfy the size requirements. There are 47 (36 H + 11 S) secondary structure elements in 1bgx_T, of which 6 satisfy the size requirements. 5.11068 [ 5.01012] ((2 . 1) (3 . 2) (6 . 4) (9 . 5)) 5.354 {2/4:6} B:0 5.11071 [ 5.01016] ((3 . 2) (5 . 3) (6 . 4) (9 . 5)) 6.736 {1/2:6} B:0 SIMILARITY (1/min{score1}): 0.1957 [and 1/min{score2}: 0.1996] [6198, 4487]: Comparing 1v8p_A and 1o4w_A, based on their crossing files. There are 12 (8 H + 4 S) secondary structure elements in 1v8p_A, of which 11 satisfy the size requirements. There are 11 (6 H + 5 S) secondary structure elements in 1o4w_A, of which 10 satisfy the size requirements. 1.38966 [ 1.26938] ((1 . 1) (2 . 2) (4 . 4) (5 . 5) (6 . 6) (9 . 8) (10 . 9) (11 . 10)) 3.521 {1/16:28} B:0 1.70498 [ 1.66812] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (9 . 8) (10 . 9) (11 . 10)) 3.865 {3/19:36} B:0 2.84082 [ 2.61834] ((8 . 2) (9 . 3) (10 . 4) (12 . 6)) 10.980 {1/6:6} B:0 3.66634 [ 3.57070] ((5 . 2) (9 . 8) (10 . 9) (12 . 10)) 7.144 {1/3:6} B:0 5.02247 [ 5.01539] ((1 . 1) (2 . 5) (3 . 6) (9 . 8) (10 . 9) (11 . 10)) 5.448 {2/4:15} B:0 SIMILARITY (1/min{score1}): 0.7196 [and 1/min{score2}: 0.7878] [6198, 5721]: Comparing 1v8p_A and 1rxw_A, based on their crossing files. There are 12 (8 H + 4 S) secondary structure elements in 1v8p_A, of which 11 satisfy the size requirements. There are 23 (16 H + 7 S) secondary structure elements in 1rxw_A, of which 16 satisfy the size requirements. 2.66418 [ 3.07707] ((1 . 4) (2 . 5) (4 . 7) (6 . 9) (9 . 12) (10 . 13)) 6.013 {2/8:15} B:0 2.75022 [ 4.00007] ((6 . 9) (9 . 12) (10 . 13) (11 . 14)) 5.907 {0/1:6} B:0 2.75106 [ 4.00035] ((2 . 5) (6 . 8) (9 . 10) (11 . 12)) 8.724 {0/3:6} B:0 2.81351 [ 3.46466] ((4 . 4) (5 . 5) (6 . 6) (8 . 8) (10 . 16)) 10.316 {1/4:10} B:0 2.92511 [ 4.06116] ((1 . 13) (2 . 14) (4 . 15) (5 . 17)) 5.925 {1/5:6} B:0 SIMILARITY (1/min{score1}): 0.7270 [and 1/min{score2}: 0.5000] [6198, 5904]: Comparing 1v8p_A and 1tfr, based on their crossing files. There are 12 (8 H + 4 S) secondary structure elements in 1v8p_A, of which 11 satisfy the size requirements. There are 24 (16 H + 8 S) secondary structure elements in 1tfr, of which 11 satisfy the size requirements. 2.20003 [ 2.20003] ((4 . 4) (6 . 6) (9 . 8) (10 . 9) (11 . 10)) 3.017 {0/3:10} B:0 2.75114 [ 2.75114] ((1 . 1) (5 . 3) (9 . 6) (12 . 8)) 8.875 {0/3:6} B:0 3.13273 [ 3.13273] ((4 . 4) (6 . 6) (8 . 8) (10 . 11)) 7.952 {1/4:6} B:0 3.66645 [ 3.66645] ((4 . 1) (5 . 2) (6 . 3) (12 . 8)) 7.990 {1/3:6} B:0 4.29705 [ 4.29705] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (6 . 6) (9 . 8) (10 . 9) (11 . 10)) 4.800 {6/14:28} B:0 SIMILARITY (1/min{score1}): 0.7127 [and 1/min{score2}: 0.7127] [6198, 6198]: Comparing 1v8p_A and 1v8p_A, based on their crossing files. There are 12 (8 H + 4 S) secondary structure elements in 1v8p_A, of which 11 satisfy the size requirements. There are 12 (8 H + 4 S) secondary structure elements in 1v8p_A, of which 11 satisfy the size requirements. 1.00000 [ 1.00000] ((1 . 1) (2 . 2) (3 . 3) (4 . 4) (5 . 5) (6 . 6) (8 . 8) (9 . 9) (10 . 10) (11 . 11) (12 . 12)) 0.000 {0/43:55} B:0 5.11090 [ 5.11090] ((3 . 6) (5 . 8) (6 . 9) (9 . 12)) 9.611 {1/2:6} B:0 5.11090 [ 5.11090] ((6 . 3) (8 . 5) (9 . 6) (12 . 9)) 9.611 {1/2:6} B:0 6.71453 [ 6.71453] ((5 . 2) (6 . 3) (9 . 6) (12 . 9)) 9.863 {2/3:6} B:0 6.71453 [ 6.71453] ((2 . 5) (3 . 6) (6 . 9) (9 . 12)) 9.863 {2/3:6} B:0 SIMILARITY (1/min{score1}): 1.0000 [and 1/min{score2}: 1.0000] [6198, 6348]: Comparing 1v8p_A and 1xo1_A, based on their crossing files. There are 12 (8 H + 4 S) secondary structure elements in 1v8p_A, of which 11 satisfy the size requirements. There are 21 (15 H + 6 S) secondary structure elements in 1xo1_A, of which 11 satisfy the size requirements. 2.20012 [ 2.20012] ((1 . 1) (4 . 4) (6 . 6) (9 . 10) (10 . 11)) 4.261 {0/3:10} B:0 2.75029 [ 2.75029] ((1 . 9) (2 . 10) (4 . 11) (5 . 13)) 6.321 {0/2:6} B:0 2.75072 [ 2.75072] ((1 . 9) (3 . 10) (4 . 11) (5 . 13)) 7.911 {0/1:6} B:0 2.75164 [ 2.75164] ((1 . 4) (3 . 6) (5 . 8) (9 . 13)) 9.728 {0/1:6} B:0 2.84016 [ 2.84016] ((8 . 2) (9 . 3) (10 . 4) (12 . 6)) 10.132 {1/6:6} B:0 SIMILARITY (1/min{score1}): 0.7138 [and 1/min{score2}: 0.7138] -------------------------------------------------------------------------------------------------------------------------